Protein Detection by Nanopores Equipped with Aptamers

Rotem, Dvir; Jayasinghe, Lakmal; Salichou, Maria; Bayley, Hagan

doi:10.1021/ja2105653

Cited by 287 publications

(304 citation statements)

References 50 publications

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“…[15][16][17][18] Biologically motivated protein detection mechanisms were tested by attaching DNA and RNA aptamers to nanopores in order to selectively detect proteins. [19][20][21][22] The quantity and spectrum of research demonstrates that protein detection with nanopores is a viable technique currently attracting academic interest. Because of its sensitivity and parallelization ability, even the sequencing of long DNA strands are now possible.…”

Section: Introductionmentioning

confidence: 99%

Probing the size of proteins with glass nanopores

et al. 2014

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a Single molecule studies using nanopores have gained attention due to the ability to sense single molecules in aqueous solution without the need to label them. In this study, short DNA molecules and proteins were detected with glass nanopores, whose sensitivity was enhanced by electron reshaping which decreased the nanopore diameter and created geometries with a reduced sensing length. Further, proteins having molecular weights (MW) ranging from 12 kDa to 480 kDa were detected, which showed that their corresponding current peak amplitude changes according to their MW. In the case of the 12 kDa ComEA protein, its DNA-binding properties to an 800 bp long DNA molecule was investigated. Moreover, the influence of the pH on the charge of the protein was demonstrated by showing a change in the translocation direction. This work emphasizes the wide spectrum of detectable molecules using nanopores from glass nanocapillaries, which stand out because of their inexpensive, lithography-free, and rapid manufacturing process.

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Section: Introductionmentioning

confidence: 99%

Probing the size of proteins with glass nanopores

et al. 2014

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“…Aptamers are generated through the process of SELEX (Systematic Evolution of Ligands by Exponential Enrichment) [38][39] or by CLADE (Closed Loop Aptameric Directed Evolution) [40]. More recent technologies to incorporate aptamers as the target capture probe are Resistive Pulse Sensing [41] and its variant technology Tunable Resistive Pulse Sensing [42]. Rotem and colleagues [41] attached an aptamer for thrombin to ἀ-haemolysin nanopore and observed the interaction between the aptamer and its target molecule thrombin by RPS.…”

Section: Trps In the Analysis Of Nanoparticle Bound Aptamer Interactimentioning

confidence: 99%

“…More recent technologies to incorporate aptamers as the target capture probe are Resistive Pulse Sensing [41] and its variant technology Tunable Resistive Pulse Sensing [42]. Rotem and colleagues [41] attached an aptamer for thrombin to ἀ-haemolysin nanopore and observed the interaction between the aptamer and its target molecule thrombin by RPS. Using this approach, they were able to detect the target molecule at nanomolar concentration.…”

Section: Trps In the Analysis Of Nanoparticle Bound Aptamer Interactimentioning

confidence: 99%

Tunable Resistive Pulse Sensing: Potential Applications in Nanomedicine

Sivakumaran

Platt

2016

Nanomedicine (Lond.)

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An accurate characterisation of nanomaterials used in clinical diagnosis and therapeutics is of paramount importance to realise the full potential of nanotechnology in medicine and to avoid unexpected and potentially harmful toxic effects due to these materials. A number of technical modalities are currently in use to study the physical, chemical and biological properties of nanomaterials but they all have advantages and disadvantages. In this review, we discuss the potential of a relative newcomer, Tunable Resistive Pulse Sensing (TRPS), for the characterisation of nanomaterials and its applications in nanodiagnostics.

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“…In some cases, the inner wall of the nanopore is engineered with other biomaterials to mimic the biological ion channels [29]. Lipid coated nanopore has been used to tailor protein translocation [30], aptamer coating on nanopore wall has been used for increased selectivity [31], chemical modification and metallization have been done for stochastic sensing of proteins [26]. The structural integrity of proteins is a common concern during the nanopore-based detection process [15].…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Study of Protein Deformation through Solid-State Nanopore

Hasan¹,

Mahmood²,

Khanzada³

et al. 2016

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Electrophoretic translocation through solid-state nanopores is a promising technique for identification of specific proteins and protein complexes. In a typical protein detection experiment, an external electric field (e-field) is applied across the nanopore and the ionic current is measured while the molecule passes through the pore. It is very important that the protein retains its structure and functionality under applied e-field and experimental conditions. However, the elongation and deformation of the 3D structure may bias the detection scheme. This work presents a theoretical assessment of protein deformation in a nanopore experiment due to applied e-field. We used nanoscale molecular dynamics (NAMD) simulations to investigate the deformation of a model protein during translocation through a silicon nitride nanopore in an aqueous solution under varying e-fields. We simulated the experimental conditions and performed quantitative analysis of the variations in thrombin protein's 3D structure. No mechanical force was applied on the protein to ensure the sole contribution of e-field on the deformation. The conformational changes of thrombin's structure were quantified in terms of root mean square deviation (RMSD) and radial distribution function. It was observed that large voltages resulted in deformations in protein structure. The protein molecule got stretched under the influence of high e-field as it traveled through nanopore. The interaction mechanism between nanopore and protein is crucial to understand the detection dynamics. The results can guide better design of experiments with proteins confined in a nanopore.

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Protein Detection by Nanopores Equipped with Aptamers

Cited by 287 publications

References 50 publications

Probing the size of proteins with glass nanopores

Probing the size of proteins with glass nanopores

Tunable Resistive Pulse Sensing: Potential Applications in Nanomedicine

Molecular Dynamics Study of Protein Deformation through Solid-State Nanopore

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